Structure

Physi-Chem Properties

Molecular Weight:  201.21
Volume:  235.895
LogP:  3.537
LogD:  3.086
LogS:  -3.407
# Rotatable Bonds:  9
TPSA:  46.25
# H-Bond Aceptor:  2
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.563
Synthetic Accessibility Score:  2.763
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.692
MDCK Permeability:  2.2352231098921038e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.473
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.97
30% Bioavailability (F30%):  0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.203
Plasma Protein Binding (PPB):  76.26791381835938%
Volume Distribution (VD):  0.857
Pgp-substrate:  23.987449645996094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.641
CYP1A2-substrate:  0.359
CYP2C19-inhibitor:  0.085
CYP2C19-substrate:  0.738
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.084
CYP2D6-inhibitor:  0.365
CYP2D6-substrate:  0.724
CYP3A4-inhibitor:  0.101
CYP3A4-substrate:  0.154

ADMET: Excretion

Clearance (CL):  7.713
Half-life (T1/2):  0.289

ADMET: Toxicity

hERG Blockers:  0.19
Human Hepatotoxicity (H-HT):  0.11
Drug-inuced Liver Injury (DILI):  0.055
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.832
Maximum Recommended Daily Dose:  0.034
Skin Sensitization:  0.727
Carcinogencity:  0.064
Eye Corrosion:  0.971
Eye Irritation:  0.454
Respiratory Toxicity:  0.955

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC29222

Natural Product ID:  NPC29222
Common Name*:   Clavaminol A
IUPAC Name:   (2R,3S)-2-aminododecan-3-ol
Synonyms:  
Standard InCHIKey:  AGYWAEBSOUKZJQ-NEPJUHHUSA-N
Standard InCHI:  InChI=1S/C12H27NO/c1-3-4-5-6-7-8-9-10-12(14)11(2)13/h11-12,14H,3-10,13H2,1-2H3/t11-,12+/m1/s1
SMILES:  CCCCCCCCC[C@@H]([C@@H](C)N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL226604
PubChem CID:   16739261
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002460] Alkanolamines
            • [CHEMONTID:0001897] 1,2-aminoalcohols

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO23165 Clavelina phlegraea Species Clavelinidae Eukaryota n.a. n.a. n.a. PMID[17336534]
NPO23165 Clavelina phlegraea Species Clavelinidae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT196 Cell Line AGS Homo sapiens IC50 = 5.0 ug.mL-1 PMID[544253]
NPT15 Cell Line Jurkat Homo sapiens Activity = 44.6 % PMID[544253]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 15400.0 nM PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 10800.0 nM PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 12500.0 nM PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 18200.0 nM PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 7.8 ug.mL-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 3.9 ug.mL-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 1.9 ug.mL-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 15.6 ug.mL-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 31.2 ug.mL-1 PMID[544255]
NPT610 Others Molecular identity unknown MIC = 31.2 ug.mL-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 62.5 ug.mL-1 PMID[544255]
NPT610 Others Molecular identity unknown MIC = 15.6 ug.mL-1 PMID[544255]
NPT610 Others Molecular identity unknown MIC = 7.8 ug.mL-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MBC = 15.6 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MBC = 7.8 ug ml-1 PMID[544255]
NPT20 Organism Candida albicans Candida albicans MFC = 62.5 ug ml-1 PMID[544255]
NPT20 Organism Candida albicans Candida albicans MFC = 31.2 ug ml-1 PMID[544255]
NPT188 Organism Candida parapsilosis Candida parapsilosis MFC = 62.5 ug ml-1 PMID[544255]
NPT554 Organism Candida glabrata Candida glabrata MFC = 31.2 ug ml-1 PMID[544255]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii MFC = 15.6 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 4.2 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 4.3 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 2.2 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 0.8 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 8.6 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 5.2 ug ml-1 PMID[544255]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. INH = 3.6 ug ml-1 PMID[544255]
NPT27631 ORGANISM Candida aaseri Candida aaseri MFC = 62.5 ug ml-1 PMID[544255]
NPT27632 ORGANISM Issatchenkia hanoiensis Issatchenkia hanoiensis MFC = 62.5 ug ml-1 PMID[544255]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC29222 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC96966
1.0 High Similarity NPC121062
0.9167 High Similarity NPC474322
0.9167 High Similarity NPC123814
0.8462 Intermediate Similarity NPC8979
0.8302 Intermediate Similarity NPC302569
0.8302 Intermediate Similarity NPC168308
0.8 Intermediate Similarity NPC319131
0.7719 Intermediate Similarity NPC17455
0.7547 Intermediate Similarity NPC270041
0.7414 Intermediate Similarity NPC47333
0.7255 Intermediate Similarity NPC193872
0.7213 Intermediate Similarity NPC113224
0.7091 Intermediate Similarity NPC471423
0.7091 Intermediate Similarity NPC471442
0.6984 Remote Similarity NPC268922
0.6875 Remote Similarity NPC475694
0.6875 Remote Similarity NPC473710
0.6842 Remote Similarity NPC471605
0.6842 Remote Similarity NPC471443
0.6825 Remote Similarity NPC471418
0.6818 Remote Similarity NPC319034
0.6818 Remote Similarity NPC193062
0.6818 Remote Similarity NPC1748
0.6818 Remote Similarity NPC66124
0.6818 Remote Similarity NPC72324
0.6786 Remote Similarity NPC471917
0.6769 Remote Similarity NPC476694
0.6769 Remote Similarity NPC476695
0.6769 Remote Similarity NPC306973
0.6769 Remote Similarity NPC476696
0.6727 Remote Similarity NPC470664
0.6613 Remote Similarity NPC474928
0.661 Remote Similarity NPC233364
0.661 Remote Similarity NPC471421
0.6607 Remote Similarity NPC277072
0.6607 Remote Similarity NPC178263
0.6591 Remote Similarity NPC267243
0.6591 Remote Similarity NPC122962
0.6591 Remote Similarity NPC145217
0.6591 Remote Similarity NPC84444
0.6557 Remote Similarity NPC145627
0.6522 Remote Similarity NPC97967
0.6508 Remote Similarity NPC286851
0.6508 Remote Similarity NPC303798
0.6441 Remote Similarity NPC204709
0.6418 Remote Similarity NPC474468
0.6415 Remote Similarity NPC289484
0.6415 Remote Similarity NPC319709
0.6393 Remote Similarity NPC474014
0.6393 Remote Similarity NPC30126
0.6393 Remote Similarity NPC57846
0.6383 Remote Similarity NPC474914
0.6383 Remote Similarity NPC474392
0.6377 Remote Similarity NPC3094
0.6377 Remote Similarity NPC477002
0.6364 Remote Similarity NPC24506
0.6364 Remote Similarity NPC163556
0.6364 Remote Similarity NPC236797
0.6364 Remote Similarity NPC112242
0.6364 Remote Similarity NPC141902
0.6364 Remote Similarity NPC147096
0.6364 Remote Similarity NPC225783
0.6364 Remote Similarity NPC50457
0.6364 Remote Similarity NPC185041
0.6349 Remote Similarity NPC223386
0.6349 Remote Similarity NPC75435
0.6349 Remote Similarity NPC471892
0.6349 Remote Similarity NPC142290
0.6349 Remote Similarity NPC198341
0.6349 Remote Similarity NPC471780
0.6333 Remote Similarity NPC290106
0.6333 Remote Similarity NPC143809
0.6333 Remote Similarity NPC216415
0.6333 Remote Similarity NPC76726
0.6333 Remote Similarity NPC193593
0.6333 Remote Similarity NPC476537
0.6316 Remote Similarity NPC272396
0.625 Remote Similarity NPC69798
0.625 Remote Similarity NPC101746
0.625 Remote Similarity NPC473952
0.625 Remote Similarity NPC77191
0.625 Remote Similarity NPC116377
0.625 Remote Similarity NPC277333
0.623 Remote Similarity NPC68974
0.6222 Remote Similarity NPC126915
0.619 Remote Similarity NPC55068
0.619 Remote Similarity NPC471419
0.619 Remote Similarity NPC163134
0.6154 Remote Similarity NPC59221
0.6143 Remote Similarity NPC140327
0.6143 Remote Similarity NPC51055
0.6143 Remote Similarity NPC212008
0.6143 Remote Similarity NPC62293
0.6136 Remote Similarity NPC110884
0.6129 Remote Similarity NPC62507
0.6129 Remote Similarity NPC8087
0.6111 Remote Similarity NPC475363
0.6111 Remote Similarity NPC473971
0.6111 Remote Similarity NPC473972
0.6094 Remote Similarity NPC41429
0.6087 Remote Similarity NPC291158
0.6087 Remote Similarity NPC205141
0.6087 Remote Similarity NPC272998
0.6087 Remote Similarity NPC181516
0.6087 Remote Similarity NPC139131
0.6087 Remote Similarity NPC185538
0.6061 Remote Similarity NPC74555
0.6061 Remote Similarity NPC266242
0.6061 Remote Similarity NPC254617
0.6061 Remote Similarity NPC306763
0.6061 Remote Similarity NPC195165
0.6032 Remote Similarity NPC150680
0.6032 Remote Similarity NPC218150
0.6032 Remote Similarity NPC22774
0.6032 Remote Similarity NPC69669
0.6032 Remote Similarity NPC306462
0.6032 Remote Similarity NPC2432
0.6 Remote Similarity NPC278209
0.6 Remote Similarity NPC311668
0.6 Remote Similarity NPC65832
0.6 Remote Similarity NPC10262
0.6 Remote Similarity NPC28394
0.6 Remote Similarity NPC31557
0.597 Remote Similarity NPC475127
0.597 Remote Similarity NPC475715
0.597 Remote Similarity NPC473419
0.5962 Remote Similarity NPC222078
0.5946 Remote Similarity NPC79367
0.5942 Remote Similarity NPC55274
0.5932 Remote Similarity NPC470666
0.5909 Remote Similarity NPC159845
0.5909 Remote Similarity NPC184150
0.5909 Remote Similarity NPC279895
0.5909 Remote Similarity NPC141156
0.5909 Remote Similarity NPC313882
0.5902 Remote Similarity NPC176164
0.5902 Remote Similarity NPC189301
0.5902 Remote Similarity NPC190385
0.5893 Remote Similarity NPC324825
0.5893 Remote Similarity NPC270805
0.5893 Remote Similarity NPC93888
0.5893 Remote Similarity NPC316231
0.5893 Remote Similarity NPC112890
0.5882 Remote Similarity NPC115800
0.5882 Remote Similarity NPC163538
0.5857 Remote Similarity NPC26932
0.5846 Remote Similarity NPC233034
0.5821 Remote Similarity NPC474469
0.5806 Remote Similarity NPC254541
0.5797 Remote Similarity NPC477200
0.5797 Remote Similarity NPC137554
0.5797 Remote Similarity NPC255535
0.5797 Remote Similarity NPC285014
0.5797 Remote Similarity NPC299603
0.5797 Remote Similarity NPC28959
0.5781 Remote Similarity NPC470665
0.5769 Remote Similarity NPC241279
0.5758 Remote Similarity NPC474402
0.5758 Remote Similarity NPC12514
0.5758 Remote Similarity NPC315980
0.5758 Remote Similarity NPC294883
0.5745 Remote Similarity NPC152759
0.5745 Remote Similarity NPC12231
0.5741 Remote Similarity NPC118459
0.5741 Remote Similarity NPC327698
0.5733 Remote Similarity NPC207657
0.5714 Remote Similarity NPC320936
0.5686 Remote Similarity NPC471282
0.5672 Remote Similarity NPC129100
0.5672 Remote Similarity NPC291650
0.5672 Remote Similarity NPC322801
0.5641 Remote Similarity NPC125253
0.5641 Remote Similarity NPC253975
0.5641 Remote Similarity NPC192025
0.5634 Remote Similarity NPC208657
0.5625 Remote Similarity NPC112398
0.56 Remote Similarity NPC74352
0.56 Remote Similarity NPC177022

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC29222 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9565 High Similarity NPD3214 Discontinued
0.9167 High Similarity NPD3215 Phase 1
0.6415 Remote Similarity NPD3211 Approved
0.623 Remote Similarity NPD9239 Approved
0.623 Remote Similarity NPD9240 Approved
0.6226 Remote Similarity NPD1152 Phase 2
0.619 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6182 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6111 Remote Similarity NPD399 Approved
0.6111 Remote Similarity NPD398 Approved
0.6111 Remote Similarity NPD400 Approved
0.6087 Remote Similarity NPD2272 Approved
0.6087 Remote Similarity NPD5383 Approved
0.6032 Remote Similarity NPD9027 Phase 3
0.6032 Remote Similarity NPD9026 Phase 2
0.6032 Remote Similarity NPD9029 Phase 3
0.6032 Remote Similarity NPD9676 Phase 3
0.6032 Remote Similarity NPD9028 Phase 2
0.5902 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5893 Remote Similarity NPD9044 Approved
0.5893 Remote Similarity NPD8624 Approved
0.5873 Remote Similarity NPD393 Approved
0.5849 Remote Similarity NPD9062 Phase 2
0.5846 Remote Similarity NPD9440 Discontinued
0.5714 Remote Similarity NPD3187 Discontinued
0.5714 Remote Similarity NPD9455 Approved
0.5672 Remote Similarity NPD9032 Approved
0.5672 Remote Similarity NPD9031 Approved
0.5672 Remote Similarity NPD9033 Approved
0.5672 Remote Similarity NPD9030 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data